5WB2

US28 bound to engineered chemokine CX3CL1.35 and nanobodies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy.

Miles, T.F.Spiess, K.Jude, K.M.Tsutsumi, N.Burg, J.S.Ingram, J.R.Waghray, D.Hjorto, G.M.Larsen, O.Ploegh, H.L.Rosenkilde, M.M.Garcia, K.C.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.35850
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human cytomegalovirus has hijacked and evolved a human G-protein-coupled receptor into US28, which functions as a promiscuous chemokine 'sink' to facilitate evasion of host immune responses. To probe the molecular basis of US28's unique ligand cross- ...

    Human cytomegalovirus has hijacked and evolved a human G-protein-coupled receptor into US28, which functions as a promiscuous chemokine 'sink' to facilitate evasion of host immune responses. To probe the molecular basis of US28's unique ligand cross-reactivity, we deep-sequenced CX3CL1 chemokine libraries selected on 'molecular casts' of the US28 active-state and find that US28 can engage thousands of distinct chemokine sequences, many of which elicit diverse signaling outcomes. The structure of a G-protein-biased CX3CL1-variant in complex with US28 revealed an entirely unique chemokine amino terminal peptide conformation and remodeled constellation of receptor-ligand interactions. Receptor signaling, however, is remarkably robust to mutational disruption of these interactions. Thus, US28 accommodates and functionally discriminates amongst highly degenerate chemokine sequences by sensing the steric bulk of the ligands, which distort both receptor extracellular loops and the walls of the ligand binding pocket to varying degrees, rather than requiring sequence-specific bonding chemistries for recognition and signaling.


    Organizational Affiliation

    Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, United States.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Science, University of Copenhagen, Denmark, Europe.,Department of Structural Biology, Stanford University School of Medicine, Stanford, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope protein US28, nanobody 7 fusion protein
A
460Human cytomegalovirus (strain Towne)Mutation(s): 0 
Gene Names: US28
Find proteins for P69333 (Human cytomegalovirus (strain Towne))
Go to UniProtKB:  P69333
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CX3CL1 protein
B
76Homo sapiensMutation(s): 0 
Gene Names: CX3CL1 (FKN, NTT, SCYD1)
Find proteins for P78423 (Homo sapiens)
Go to Gene View: CX3CL1
Go to UniProtKB:  P78423
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
nanobody B1
D
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
PCA
Query on PCA
D
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 47.170α = 90.00
b = 128.940β = 90.00
c = 127.740γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM097015

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references